RetrogeneDB ID: retro_mmul_1838

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:70183461..70184821(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019436
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM117A
• Ensembl ID: ENSMMUG00000008871
• Aliases: None
• Description: None

Sequence

>retro_mmul_1838
ATGGCAGGGGCCGCAGCGGGCGGCAGAGGCGGAGGTGCCTGGGGGCCGGGGCGCGGAGGGTCGGGGGTGCTCCGACGGGG
CTGCTCTCCCCCAGCCCCCGCCGGCTCCCCGCGGGCTGGGCTGCCGCCGCTCAGGGCCACGATCCCCTTCCAGCTGCAGC
AGCCGCACCAGCGCCGGGACGGGGGTGGCCGTGCAGCCAGCGTCCCATGCTCGGTGGCCCCAGAAAAGTCAGTGTCTAGG
CCTCAGCCACTTCAGGTCCGGCGTACATTCTCCCTGGACACCATCCTCAGCTCCTACCTTCCGAGCCAGTGGCCACGAGA
TGCTGATGGGGCCTTCACCTGCTGCACCAATGACAAGGCCACCCAGACACCCCTGTCCTGGCAAGAGCTAGAAGGTGAGC
GTGCCAGCTCCTGTGCACACAAGCGCTCAGCATCCTGGGGCAGCACAGACCACCGAAAAGAGATTTCCAAGTTGAAGCAA
CAACTGCAGAGGACAAAAGCTGAGCCGCAGTGGGAAAGAGAAGGAGCGAGGTTCCCTACTCCCAGGGGACCACGCAGTGC
GGGGAGCGCTGAGGGCGTCCCCTCCCAGCTTCCCCTCAGGGTCCCCTGTCTTGCGACTCAGCCCCTGCCTGCACAGGAGC
CTGGAAGGGCTCAACCAAGAGCTGGAGGAGGTGTTTGTGAAGGAGCAGGGAGAAGAGGAGCTGCTGAGGATCCTTGAGAT
CCCTGATGGGAACCGGGCCCCAGCTCCTCCCCAGAGTGGCAGCTGTGATCATCCCCTCCTCCTCCTGGAGTCTGGCAACC
TTGCCAGCTCTCCTTCCATTTCCTTGGCATCCCCCCAGCCTTGTGGCCCGGCCAGTCATGAGGAACACCGGGGTGCCGCC
GAGGAGCTGGCATCCACCCCCAACGACAAAGCCTCCTCTCCAGGCCACCCAGCCTTTCTTGAAGATGGCAGCCCATCTCC
TGTCCTTGCCTTTGCTGCCTCCCCTCGGCCTAATCATAGCTACGTCTTCAAACGGGAGCCCCCAGAAGGCTGTGAGAAAG
TGCGTGTGTTTGAAGAAGCCACGTCCCCAGGTCCTGACCCGGCCTTCCTGACTTCCTGTCCTGACAAGAACAAAGTCCAT
TTCAACCCGACCGGCTCAGCCTTCTGCCCCGTCAACCTGATGAAGCCCCTCTTCCCTGGCATGGGCTTCATCTTCCGTAA
CTGCCCCTCAAACCCGGGGTCTCCCCTTCCCCCGGCCAGACCCAGGCCACCACCTCGGAAGGATCCGGAGGCCTCCAAGG
CCTCCCCACTGCCCTTCGAGCCATGGCAGTGCACCCCACCATCAGAAGAGTCTGTGCTTTTCCAGAGCTCCCTGATGGTC

Alignment

ORF - retro_mmul_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGAAAGGRGGGAWGPGRGGSGGLRRGCSPPAPAGSPRAGLQPLRATIPFQLQQPHQRRDGGGRAASVPC
          MAGAAAGGRGGGAWGPGRGGSG.LRRGCSPPAPAGSPRAGL.PLRATIPFQLQQPHQRRDGGGRAASVPC
Retrocopy MAGAAAGGRGGGAWGPGRGGSGVLRRGCSPPAPAGSPRAGLPPLRATIPFQLQQPHQRRDGGGRAASVPC

Parental  SVAPEKSVSRPQPLQVRRTFSLDTILSSYLLGQWPRDADGAFTCCTNDKATQTPLSWQELEGERASSCAH
          SVAPEKSVSRPQPLQVRRTFSLDTILSSYL..QWPRDADGAFTCCTNDKATQTPLSWQELEGERASSCAH
Retrocopy SVAPEKSVSRPQPLQVRRTFSLDTILSSYLPSQWPRDADGAFTCCTNDKATQTPLSWQELEGERASSCAH

Parental  KRSASWGSTDHRKEISKLKQQLQRTK-LSRSGKEKERGSPLPGDHAVRGALRASPPSFPSGSPVLRLSPC
          KRSASWGSTDHRKEISKLKQQLQRTK.LSRSGKEKERGS.LPGDHAVRGALRASPPSFPSGSPVLRLSPC
Retrocopy KRSASWGSTDHRKEISKLKQQLQRTK>LSRSGKEKERGSLLPGDHAVRGALRASPPSFPSGSPVLRLSPC

Parental  LHRSLEGLNQELEEVFVKEQGEEELLRILEIPDGHRAPAPPQSGSCDHPLLLLEPGNLASSPSMSLASPQ
          LHRSLEGLNQELEEVFVKEQGEEELLRILEIPDG.RAPAPPQSGSCDHPLLLLE.GNLASSPS.SLASPQ
Retrocopy LHRSLEGLNQELEEVFVKEQGEEELLRILEIPDGNRAPAPPQSGSCDHPLLLLESGNLASSPSISLASPQ

Parental  PCGPASHEEHRGAAEELASTPNDKASSPGHPAFLEDGSPSPVLAFAASPRPNHSYVFKREPPEGCEKVRV
          PCGPASHEEHRGAAEELASTPNDKASSPGHPAFLEDGSPSPVLAFAASPRPNHSYVFKREPPEGCEKVRV
Retrocopy PCGPASHEEHRGAAEELASTPNDKASSPGHPAFLEDGSPSPVLAFAASPRPNHSYVFKREPPEGCEKVRV

Parental  FEEATSPGPDLAFLTSCPDKNKVHFNPTGSAFCPVSLMKPLFPGMGFIFRNCPSNPGSPLPPASPRPPPR
          FEEATSPGPD.AFLTSCPDKNKVHFNPTGSAFCPV.LMKPLFPGMGFIFRNCPSNPGSPLPPA.PRPPPR
Retrocopy FEEATSPGPDPAFLTSCPDKNKVHFNPTGSAFCPVNLMKPLFPGMGFIFRNCPSNPGSPLPPARPRPPPR

Parental  KDPEASKASPLPFEPWQRTPPSEESVLFQSSLMV
          KDPEASKASPLPFEPWQ.TPPSEESVLFQSSLMV
Retrocopy KDPEASKASPLPFEPWQCTPPSEESVLFQSSLMV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	2.80 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.81 RPM
SRP007412_cerebellum	0.26 RPM	12.27 RPM
SRP007412_heart	0.06 RPM	7.24 RPM
SRP007412_kidney	0.00 RPM	8.33 RPM
SRP007412_liver	0.04 RPM	5.78 RPM
SRP007412_testis	0.38 RPM	26.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1838 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1838 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000008871	1 retrocopy	retro_mmul_1838 ,